MySQL has a feature that allows you to log slow running queries to a file. To enable you just need to add some lines to your my.cnf file, and restart.

Insert the following into /etc/my.cnf:

log-slow-queries = /var/log/mysql/mysql-slow.log
long_query_time = 5

Save my.cnf and do the following when you return to a shell:

#touch /var/log/mysql/mysql-slow.log
#chown mysql:mysql /var/log/mysql/mysql-slow.log
#service mysql restart

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